If you use the remote blast service at the EBI you should refer to:Web services at the European Bioinformatics Institute-2009
Nucl. Acids Res. (2009) doi: 10.1093/nar/gkp302 A new bioinformatics analysis tools framework at EMBL-EBI
Nucl. Acids Res. (2010) 38 (suppl 2): W695-W699. doi: 10.1093/nar/gkq313

If you use PISA you should refer to:Inference of macromolecular assemblies from crystalline state.
E. Krissinel and K. Henrick (2007).J. Mol. Biol.372, 774-797.